SOLVATION - MOLECULAR-DYNAMICS STUDY OF A DIPEPTIDE IN WATER

A molecular dynamics study of a dilute aqueous solution of an alanine dipeptide in the C7eqconfiguration has been carried out. The intermolecular potentials are given by a sum of pairwise additive Lennard-Jones and electrostatic terms : the peptide internal degrees of freedom arc governed by an empirical energy function; and the water molecules are described by a modification of the ST2 model of Stillinger and Rahman which includes internal flexibility. The average local structure of the dipeptide and the dynamics of its internal structural fluctuations arc affected very little by the prcsencc of the solvent; the only evidence for rapidly damped dynamic correlations is found for the lowest frequency motions (dihedral angle torsions; (ω~ 50 cm-1) and for those involving the the lightest masses (methyl group libration; ω~-185 cm-1). Analysis of the kinetic properties of the solvent shows that the influence of the solute is limited to the first solvation layer. Although the polar (C=O, NH) groups of the dipeptide have little influence on the mobility of the solvent, that near the nonpolar methyl groups is substantially hindered in both its translational and rotational motion. Consideration of the bonding and geometric disposition of the solvent molecules shows that the mobility loss near nonpolar groups is due to the maintenance of bulk-like hydrogen bonding within the constraint nf a reduced number of possible bonding neighbors. For solvent molecules near polar dipeptide groups, this constraint is not present since water-dipeptide as well as water-water hydrogen bonds can form. It is pointed out that significant contributions to the enthalpy of solution and the solute partial molar heat capacity can result from small changes in the energetics of solvent-solvent hydrogen bonding. Further, although clathrate-like geometric characteristics are found near nonpolar groups, a description implying solid-like attributes is very misleading. © 1979, American Chemical Society. All rights reserved.